These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Harsher in Hindsight: Stalker's wife describes his crippled daughter as "a gift from The Zone." The locations for the outdoor scenes were heavily polluted, and several people on the crew suffered illnesses and untimely deaths.
True Art Is Incomprehensible: The utter lack of exposition makes the entire film open to a wide variety of interpretations (though it does follow the basic plot and themes of the novel fairly faithfully).
The Woobie: Stalker bemoans the lack of 'magic' in the modern world, gets upset when people fail to pay the Zone appropriate respect, and generally walks around halfway between panicky tears and childish stroppiness.
Adaptation Displacement: Most players are unaware of the novel and the film. The ones that are bought it because of the novel and the film. The rest of us bought the novel and the film because of the game.
And even fewer people know that the game is also partially based on another short story of the Strugatsky Brothers, The Forgotten Experiment (which features concepts of quasi-natural yet explained origin of the Zone and scientists working in the Zone).
Character Alignment: The factions have distinguishable alignments that set them apart from other factions:
Duty: Type 2 Lawful Neutral by default, though they claim to be Type 1 Lawful Good. However, a few number of their members (such as Morgan from Call of Pripyat) have been known to be Type 2 Lawful Evil.
Mercenaries: Ranges from Type 2 Chaotic Evil (the Shadow of Chernobyl and Clear Sky mercs) to Type 1 Neutral Evil (the mercs from Call of Pripyat) to Type 1 Chaotic Neutral (Hog's and Leshiy's groups in Clear Sky, and Hatchet's group in Call of Pripyat).
Monolith: As a Church Militant / Cargo Cult, they're actually Type 3 Lawful Evil since, by the C-Consciousness' orders, they don't want anyone to dig too deep into the secrets of the Zone.
Military: A mixture of Type 1 and Type 3 Lawful Evil in Shadow of Chernobyl and Clear Sky, but are Type 1 Lawful Neutral in Call of Pripyat.
Among the three protagonists, Marked One / Strelok is Neutral Good (though that's dependent on your choices in Shadow of Chernobyl and it's his default alignment in Call of Pripyat), Scar is Chaotic Neutral (since he's a mercenary), and depending how the player controls him, Major Degtyarev is either Lawful Good (if he helps out stalkers and doesn't side with the Bandits), Lawful Neutral (if he doesn't choose sides), or Lawful Evil (if he sides with the Bandits).
The Poltergeists in the Red Forest mine in Clear Sky are a subject of many angry message board rants. They basically toss metal water heaters at you which can kill you in one hit and are essentially undodgeable. Going up against them can also result in being killed by a weapon without said weapon being fired. Nothing like being telekinetically bludgeoned to death with a dropped assault rifle.
Not to mention wild dogs. You could be a top-level Stalker outfitted with exoskeleton armor and the finest of guns, but you'd still have to make a frenzied dash past the pack of wild dogs in front of the Duty compound to get in. Alternately, you could just shoot one or two. If you get lucky and kill the pack alpha, the rest of them run away.
The Poltergeists in STALKER: SOC aren't a bowl of cherries either. Sure, they can't one-hit-kill you, but you can't get rid of most of the stuff they throw, the damned things move FAST, and there are SEVEN OR EIGHT in X18, the first time you'll run into them. Aim for the center of the flying ball of sparks and be ready to heal. It also doesn't help that they can see through walls. Fortunately, they were nerfed for Call of Pripyat. Except for one poltergeist towards the end (that has ShoC's poltergeists see through walls abilities), CoP poltergeists can only see you if you're moving, so all you have to do is stand still ands they will lose sight of you. This also works for pyrogeists.
Call of Pripyat makes up for this by adding psychic dwarves who can telekinetically steal your weapon and then throw it halfway across the map. When they're not throwing gas tanks at you, that is. The burers are easy to deal with when you learn how they act: just use a knife. They can't pull the knife out the player's hands and the knife inflicts enough damage to kill it in 6-7 stabs. Just don't try it if there's a second burer nearby. Alternatively, use the RPG.
Any enemy packing an RPG in Shadow Of Chernobyl. The blast radius is big enough that you will hardly have a chance to dodge, unless you know where they are and start moving the instant they fire. Even if you dodge, you'll still get knocked around by the blast, so good luck seeing clearly enough to return fire. And of course, the RPG is heavy enough and there's little enough ammo that you can't reasonably carry it with you. Your best bet is to quicksave and try to snipe them before they see you.
Ear Worm: Several. The vocal bit for Dirge for the Planet is looped endlessly inside Sidorovich's bunker whilst the Bar used to have one of the stalker guitar songs play over and over and once you hear the Bandit Base Polka in Clear Sky it will never. Ever. Stop.
Game Breaker: When you do get one the VSS sniper rifle is one of the best guns in the game (very light, silenced, accurate, can kill most enemies in 1-2 shots, and is the only sniper rifle you can sprint with, and ammunition isn't that hard to find, at least compared to SVD and gauss rifle rounds).
The Gauss Rifle in Call of Pripyat. It can kill every human enemy in the game and can take down any mutant that is not a Pseudogiant (though it itself can be killed in 2-3 shots from the weapon). After you show Cardan the weapon and retrieve the documents concerning about the experimentation of the gun, he will offer you homemade batteries for 2000 RU each, essentially farming unlimited ammunition for your Infinity+1 Sword.
The FN F2000, H&K G36, USP .45 Compact (and the custom version "March"), Storm (unique OC-14 Groza that fires the common 5.45 ammo), AS VAL (late game at least), Strelok's rapid-fire AK-74, the VSS Vintorez and its custom variant "Tide", and the Armsel Protecta. Getting any of these weapons, however, requires you to either have a small mountain of cash, fight through a bunch of enemies, or get on good standings with a certain faction. Once you do that however, and fully upgrade them, you're more or less set for the majority of the game.
With a little bit of exploring in Clear Sky, you can pick up Scar's Vintorez within twenty minutes of starting a new game. Doesn't quite count as a Disc One Nuke, though, because it's badly damaged (having been dropped in the emission) and empty. You won't be finding ammo for it for a while, but carrying it along or stashing it for later retrieval saves you the cost of the weapon itself. Upgrade it properly and stock up on AP ammo (available from the Duty and Bandit vendors and often available on corpses) and you're pretty much set for weapons through the endgame.
Getting the Armsel is pretty easy under the right circumstances, as well - Vano's mission sends you into the middle of a camp with about twelve bandits in it to pay off his debt. You can pay off the bandit leader (who has the Armsel) and get mugged on the way out, intimidate the bandit leader (with a high-level weapon) and leave, or just murder everyone. Walking into the leader's office and shooting him in the head, before stealing his gun and using it to fight your way out, is both hilariously audacious and fun.
Certain artifacts fall into this as well. Most artifacts give increased protection against certain types of damage, but often release radiation, making it necessary to either pair them with an artifact that absorbs radiation or pop an antirad or bottle of vodka every couple minutes. Others don't. The Flash and Moonlight artifacts all give large-scale benefits to your sprint meter (wearing one Moonlight or two Flash artifacts can let you sprint indefinitely so long as you aren't overloaded on weight), and their negative effect is an increased vulnerability to electricity. Electrical anomalies are encountered maybe three times in the entire first game, and actually spawn more of these artifacts. Picking up a handful of Flash or if you're incredibly lucky, a pair of Moonlight artifacts at the Agroprom Underground is incredibly easy and makes it simple to outrun the wildlife and hostile stalkers when engagement isn't an option, and makes shuttling tons of gear back and forth a cakewalk.
Goddamned Bats: Blind Dogs and Pseudodogs. Ridiculously hard to get a headshot on, drop near-worthless parts only one trader wants (Sakharov), and TRAVEL IN PACKS. Pack a shotgun and a bunch of medkits, or suffer a death of a thousand cuts.
The same goes for the rats, although they're called hamsters. Though they lie somewhere between this trope and Demonic Spiders since even a single one of them can tear your armor surprisingly quickly.
There's also the knife's secondary attack (see the One-Hit Kill entry below).
Sadly fixed in Call of Pripyat.
If you die just as you are transitioning from one area to the next, you will spawn in dead, unable to use your weapon or access your inventory or talk to people, but mobile and completely immortal.
The armour repairing trick with four battery artifacts (Collecting at least 4 artifacts of the flame/electricity battery type, wearing them, then jumping into a fire/electrical surge will restore your HP, and more importantly and absolutely a bug and not a feature, repair your armor, otherwise impossible in the unmodded 'Shadow of Chernobyl'').
Hell Is That Noise: The distinctive wheeze-pant of Bloodsuckers, which due to their cloaking ability is the best (and often only) way to determine their location. Even hardened, seasoned players are easily unnerved by the sound, and the first time a player meets a Bloodsucker can lead to full-blown panic attacks. Also the voice of the Wish Granter, which continuously calls out to you in Chernobyl NPP.
Usually the first sign that there is a Controller around is a growl, followed by a tone which sounds like a tinnitus episode. Then comes the Interface Screw...
The low, rumbling sound that precedes any blowout in Call of Pripyat is always unsettling, and an indication that you have only a minute or two to get somewhere safe.
The weather mod used by almost every major mod for Call of Pripyat, including Complete and Misery, lengthens the blowout sound by several minutes, and it can actually be picked up surprisingly early on if you're using decent headphones or a subwoofer. This presents a new problem - differentiating the game's natural ambience or the sound of an approaching (natural) storm from the rumblings of an imminent emission. This is known to make some players incredibly paranoid.
Special Effects Failure: For some reason the sound of choppers overhead can be interrupted by breaking crates. Also the glowing eyes of the mutants can look a bit weird up close, for some reason the same effect is used for actual lights.
Spiritual Licensee There's no official connection to either Roadside Picnic or Stalker, but so much is clearly lifted from them it's often assumed the game is licensed.
Surprisingly Improved Sequel: Call of Pripyat is noticeably more polished than the previous two games, adding multiple UI improvements, removing Clear Sky's infamous homing grenades and bug-ridden Faction Wars, giving the player decent equipment from the beginning and (most importantly) making the game playable out of the box without the need for multiple patches and bug-fixing mods.
That One Level: The 2nd level of Clear Sky, where crossing into the new area by the only available route has you coming out behind a boulder, on the other side of which is a mounted machine gun in the possession of the military. Well at least they don't know I'm here - wrong; they know you're there and tell you so. Well I'll be safe behind this rock - wrong again; after a few quick bursts, they send a number of better-armed and better-armoured soldiers after you. If you manage to dispatch them, you then have to figure out which way you can safely leg it.
Once you realize that this is essentially a death-trap unless you've got at least a dozen spare medkits in your inventory (even after knocking off the squad of heavily-armored soldiers, that MG still has a ridiculous field of fire), your best bet is to just turn around, go back to the Swamps, and enter the Cordon from the northern entrance. Sure, you wind up next to a group of Loners that get pissy if you get too close, but it's the easier way in.
Shadow of Chernobyl has the Red Forest where nearly everything is radioactive, making it much harder to take cover properly. The vast majority of the trouble in that level can be bypassed if you don't follow the road and cut through the forest instead, because ninety percent of the Monolith or zombie enemies on that level are waiting for you on the road, and with the way it curves it's nearly impossible to get a shot off without taking loads of return fire. Cutting through the forest makes the level far easier, especially if you've packed a sniper rifle. Plus, once you've gotten to the other side, you can cut back and take all the Monolith troops from behind, netting yourself loads of equipment.
What Happened To The Unknown Stalker?: The unnamed stalker that rescues you in the intro of Shadow of Chernobyl is never mentioned again in either of the three games. It could be speculated that he probably went off on another quest and met an untimely demise off-screen or probably met a Fate Worse than Death.